11-61185242-C-G

Variant names:

• chr11-61185242-C-G
• rs612386
• XR_007062691.1:n.1397+2072C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062691.1(LOC124902678):​n.1397+2072C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 151,618 control chromosomes in the GnomAD database, including 35,229 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (35229 hom., cov: 31)
• Consequence: LOC124902678 XR_007062691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 2 publications found

Genes affected

LOC124902678 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902678	XR_007062691.1	n.1397+2072C>G		intron_variant	Intron 2 of 3
LOC124902678	XR_007062692.1	n.2218+2072C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100731 AN: 151502 Hom.: 35173 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.625

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.665 AC: 100845 AN: 151618 Hom.: 35229 Cov.: 31 AF XY: 0.672 AC XY: 49785 AN XY: 74082

African (AFR) AF: 0.820 AC: 33700 AN: 41092

American (AMR) AF: 0.683 AC: 10411 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1871 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5165 AN: 5182

South Asian (SAS) AF: 0.844 AC: 4054 AN: 4806

European-Finnish (FIN) AF: 0.647 AC: 6837 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36840 AN: 67958

Other (OTH) AF: 0.629 AC: 1323 AN: 2102

Alfa AF: 0.595 Hom.: 3341

Bravo AF: 0.672

Asia WGS AF: 0.914 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.47
PhyloP100		-0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs612386; hg19: chr11-60952714;